Aims: The COVID-19 containment strategy in Sweden uses public health recommendations relying on personal responsibilityfor compliance. Universities were one of few public institutions subject to strict closure, meaning that students had toadapt overnight to online teaching. This study investigates the prevalence of self-reported recommendation compliance andassociations with self-reported symptoms of contagion, self-experienced effects on mental health and academic self-efficacyamong university students in Sweden in May–June 2020. Methods: This was a cross-sectional 23 question online survey inwhich data were analysed by multinomial regression, taking a Bayesian analysis approach complemented by null hypothesistesting. Results: A total of 4495 students consented to respond. Recommendation compliance ranged between 70% and 96%.Women and older students reported higher compliance than did men and younger students. Mild to moderate COVID-19symptoms were reported by 30%, severe symptoms by fewer than 2%; 15% reported being uncertain and half of theparticipants reported no symptoms. Mental health effects were reported by over 80%, and changes in academic self-efficacywere reported by over 85%; in both these areas negative effects predominated. Self-reported symptoms and uncertaintyabout contagion were associated with non-compliance, negative mental health effects, and impaired academic self-efficacy.Conclusions: Students generally followed public health recommendations during strict closure of universities,but many reported considerable negative consequences related to mental health and academic self-efficacy.Digital interventions should be developed and evaluated to boost coping skills, build resilience and alleviatestudent suffering during the pandemic and future similar crises.